Hi Edward,
I have the Nvidia Shield TV 1st gen.
The following is more of a workaround than a true fix. I often experience the same issue. I can eventually get the remote working if I leave it on charge for a while, then try syncing it to the Nvidia again. Sometimes I have to connect the remote to the Shield TV via a usb cable to get it to recognize the remote again. I picked up the newer version of the remote (which works much better and uses AAA batteries :-) The only thing that disappointed me about the new remote is it doesn’t have a 3.5mm headphone jack, so you can’t use it to connect your headphones. I constantly have connection problems with the old remote, and old controller, so I just use the new remote with a pair of bluetooth headphones instead. If I want to play a game, I’ll just connect one of my Xbox One controllers, which work great, except their headphone jack doesn’t work with the Nvidia Shield TV.
Hope this helps.